Minor physical anomalies, together with obstetric complications, family history, and handedness status, were assessed to explore putative neurodevelopmental disturbance(s) in patients with schizophrenia whose cerebral structure had been examined previously by magnetic resonance imaging. Minor physical anomalies were related to negative symptoms in males and to premorbid intellectual function in females, but not to ventricular volume; however, three patients with evident neurodevelopmental anomalies of the ventricular system showed prominent minor physical anomalies. In exploratory analyses, obstetric complications were associated with left ventricular asymmetry, and a positive family history with inverse profiles of asymmetry in males vs. females; non-right-handedness was associated with increased ventricular volume in males but with poorer premorbid intellectual function in females. This nexus of relationships and their gender specificities suggest early dysmorphogenesis in schizophrenia that is related to sexual dimorphism.